TNRC18

trinucleotide repeat containing 18

Basic information

Region (hg38): 7:5306789-5425414

Links

ENSG00000182095 ∙ NCBI:84629 ∙ ∙ HGNC:11962 ∙ Uniprot:O15417 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TNRC18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNRC18 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				46	36	82
missense			300	18	19	337
nonsense						0
start loss						0
frameshift						0
inframe indel			1		1	2
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding					59	59
Total	0	0	301	64	115

Variants in TNRC18

This is a list of pathogenic ClinVar variants found in the TNRC18 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-5308110-C-T		not specified	Uncertain significance (Sep 29, 2023)
7-5308115-C-T			Benign (May 05, 2021)
7-5308118-G-A			Benign (May 05, 2021)
7-5308159-C-T		not specified	Uncertain significance (Apr 25, 2023)
7-5308196-C-G		not specified	Uncertain significance (Jan 31, 2022)
7-5308229-C-T			Likely benign (May 03, 2018)
7-5308283-G-A			Benign (May 05, 2021)
7-5308317-G-A			Likely benign (May 18, 2018)
7-5308345-T-TG			Benign (May 17, 2021)
7-5308851-A-C			Benign (Jun 04, 2021)
7-5308872-T-G			Likely benign (-)
7-5308893-C-G		not specified	Uncertain significance (Apr 07, 2022)
7-5308906-C-T		not specified	Uncertain significance (Mar 02, 2023)
7-5308915-G-A		not specified	Uncertain significance (Aug 02, 2021)
7-5308921-A-C		not specified	Uncertain significance (Dec 05, 2022)
7-5309094-G-A			Benign (May 15, 2021)
7-5309136-C-T			Likely benign (Apr 09, 2018)
7-5309141-G-T		not specified	Uncertain significance (Sep 21, 2021)
7-5309153-G-C			Benign (May 18, 2018)
7-5309156-C-T			Likely benign (Jul 31, 2018)
7-5309170-C-G		not specified	Uncertain significance (Jun 22, 2023)
7-5309180-G-A			Benign (Dec 31, 2019)
7-5309238-C-T		not specified	Uncertain significance (Jan 08, 2024)
7-5309304-A-G		not specified	Uncertain significance (May 08, 2024)
7-5309305-T-C		not specified	Uncertain significance (Feb 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNRC18	protein_coding	protein_coding	ENST00000430969	29	118625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00907	124619	0	12	124631	0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.262	1647	1.62e+3	1.02	0.000114	18328
Missense in Polyphen		404	388.84	1.039		4619
Synonymous	-7.12	1004	755	1.33	0.0000611	6321
Loss of Function	6.91	16	84.6	0.189	0.00000404	1148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000866	0.0000646
Ashkenazi Jewish	0.000104	0.0000993
East Asian	0.0000557	0.0000556
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.0000686	0.0000619
Middle Eastern	0.0000557	0.0000556
South Asian	0.00	0.00
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.550
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.606

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Tnrc18

Gene ontology

• Cellular component: nucleus;nucleoplasm;mitochondrion;cytosol;nuclear membrane
• Molecular function: chromatin binding